3R1R

RIBONUCLEOTIDE REDUCTASE R1 PROTEIN WITH AMPPNP OCCUPYING THE ACTIVITY SITE FROM ESCHERICHIA COLI

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.287 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding.

Eriksson, M., Uhlin, U., Ramaswamy, S., Ekberg, M., Regnstrom, K., Sjoberg, B.M., Eklund, H.

(1997) Structure 5: 1077-1092

  • Primary Citation of Related Structures:  
  • Also Cited By: 2XAZ, 2XAX, 2XAW, 2XO5, 2XO4, 2X5B, 2X59, 2X3I

  • PubMed Abstract: 

    • Ribonucleotide reductase (RNR) is an essential enzyme in DNA synthesis, catalyzing all de novo synthesis of deoxyribonucleotides. The enzyme comprises two dimers, termed R1 and R2, and contains the redox active cysteine residues, Cys462 and Cys225. T ...

    Ribonucleotide reductase (RNR) is an essential enzyme in DNA synthesis, catalyzing all de novo synthesis of deoxyribonucleotides. The enzyme comprises two dimers, termed R1 and R2, and contains the redox active cysteine residues, Cys462 and Cys225. The reduction of ribonucleotides to deoxyribonucleotides involves the transfer of free radicals. The pathway for the radical has previously been suggested from crystallographic results, and is supported by site-directed mutagenesis studies. Most RNRs are allosterically regulated through two different nucleotide-binding sites: one site controls general activity and the other controls substrate specificity. Our aim has been to crystallographically demonstrate substrate binding and to locate the two effector-binding sites.

    Related Citations: 
    • Structure of Ribonucleotide Reductase Protein R1
      Uhlin, U.,Eklund, H.
      (1994) Nature 370: 533

    Organizational Affiliation: 

    Department of Molecular Biology, Swedish University of Agricultural Sciences, Uppsala Biomedical Center, Sweden.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEOTIDE REDUCTASE R1 PROTEIN
A, B, C
761Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: nrdA (dnaF)
EC: 1.17.4.1
Find proteins for P00452 (Escherichia coli (strain K12))
Go to UniProtKB:  P00452
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RIBONUCLEOTIDE REDUCTASE R2 PROTEIN
D, E, F, P
20Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: nrdB (ftsB)
EC: 1.17.4.1
Find proteins for P69924 (Escherichia coli (strain K12))
Go to UniProtKB:  P69924
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ATP
Query on ATP
Download SDF File 
Download CCD File 
A, B, C
ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.287 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 224.610α = 90.00
b = 224.610β = 90.00
c = 336.630γ = 120.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
TNTrefinement
REFMACrefinement
DENZOdata reduction
TNTphasing

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-01-28
    Type: Initial release
  • Version 1.1: 2008-03-25
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance